A festschrift for J. Martyn Bailey, a biochemist extraordinaire

A festschrift for Dr. John Martyn Bailey, Professor of Biochemistry and Molecular Biology was organized by the Biochemistry department of the George Washington University School of Medicine and Health Sciences on December 4-5, 2006 to honor his 48 years of contributions. He made important contributions in the areas of essential fatty acids, prostaglandins, thromboxanes and lipoxygenase metabolites.     

The manzanar project: Towards a solution to poverty, hunger, environmental pollution, and global warming through sea water aquaculture and silviculture in deserts

Summary Dr. Gordon Sato is a former Editor-in-Chief of In Vitro Cellular and Developmental Biology, President of the Tissue Culture Association (now Society for In Vitro Biology), and Director of the W. Alton Jones Cell Science Center (now Adirondack Biomedical Center). He began pilot experiments on the Manzanar Project at test sites in the Salton Sea while a Professor of Biology at the University of California, San Diego and continued the project in the laboratory at the Cell Center in Lake Placid, NY and at Eritrean test sites during their war of independence. Since 1994, he spends up to 10 mo. per yr in Eritrea where he directs the Manzanar Project and trains young Eritrean scientists in the field in the area of what he refers to as “low-tech biotech.” The name of the Manzanar Project was inspired by the camp in California where Dr. Sato and his family were interned during World War II.—The Editor     

Optimal Transmission Radius for Flooding in Large Scale Sensor Networks

One of the principal characteristics of large scale wireless sensor networks is their distributed, multi-hop nature. Due to this characteristic, applications such as query propagation rely regularly on network-wide flooding for information dissemination. If the transmission radius is not set optimally, the flooded packet may be holding the transmission medium for longer periods than are necessary, reducing overall network throughput. We analyze the impact of the transmission radius on the average settling time—the time at which all nodes in the network finish transmitting the flooded packet. Our analytical model takes into account the behavior of the underlying contention-based MAC protocol, as well as edge effects and the size of the network. We show that for large wireless networks there exists an intermediate transmission radius which minimizes the settling time, corresponding to an optimal tradeoff between reception and contention times. We also explain how physical propagation models affect small wireless networks and why there is no intermediate optimal transmission radius observed in these cases. The mathematical analysis is supported and validated through extensive simulations.Marco Zuniga is currently a PhD student in the Department of Electrical Engineering at the University of Southern California. He received his Bachelors degree in Electrical Engineering from the Pontificia Universidad Catolica del Peru in 1998, and his Masters degree in Electrical Engineering from the University of Southern California in 2002. His interests are in the area of Wireless Sensor Networks in general, and more specifically in studying the interaction amongst different layers to improve the performance of these networks. He is a member of IEEE and the Phi Kappa Phi Honor society.Bhaskar Krishnamachari is an Assistant Professor in the Department of Electrical Engineering at the University of Southern California (USC), where he also holds a joint appointment in the Department of Computer Science. He received his Bachelors degree in Electrical Engineering with a four-year full-tuition scholarship from The Cooper Union for the Advancement of Science and Art in 1998. He received his Masters degree and his Ph.D. in Electrical Engineering from Cornell University in 1999 and 2002, under a four-year university graduate fellowship. Dr. Krishnamacharis previous research has included work on critical density thresholds in wireless networks, data centric routing in sensor networks, mobility management in cellular telephone systems, multicast flow control, heuristic global optimization, and constraint satisfaction. His current research is focused on the discovery of fundamental principles and the analysis and design of protocols for next generation wireless sensor networks. He is a member of IEEE, ACM and the Tau Beta Pi and Eta Kappa Nu Engineering Honor Societies     

A Concept of Educational Activity for Schoolchildren

About two years ago, on a cool Southern California day, Vasili Davydov addressed a group of social scientists at the University of California, San Diego. He began his talk with a paradox. He had come, he said, to tell us about educational activity. He promised to exhibit principles that promote educational activity, and applied programs deriving from those principles. Then he laughed. "But you'll never see educational activity in the school," he said, and laughed again.     

A flexible multi-dimensional QoS performance measure framework for distributed heterogeneous systems

When users’ tasks in a distributed heterogeneous computing environment (e.g., cluster of heterogeneous computers) are allocated resources, the total demand placed on some system resources by the tasks, for a given interval of time, may exceed the availability of those resources. In such a case, some tasks may receive degraded service or be dropped from the system. One part of a measure to quantify the success of a resource management system (RMS) in such a distributed environment is the collective value of the tasks completed during an interval of time, as perceived by the user, application, or policy maker. The Flexible Integrated System Capability (FISC) measure presented here is a measure for quantifying this collective value. The FISC measure is a flexible multi-dimensional measure such that any task attribute can be inserted and may include priorities, versions of a task or data, deadlines, situational mode, security, application- and domain-specific QoS, and task dependencies. For an environment where it is important to investigate how well data communication requests are satisfied, the data communication request satisfied can be the basis of the FISC measure instead of tasks completed. The motivation behind the FISC measure is to determine the performance of resource management schemes if tasks have multiple attributes that needs to be satisfied. The goal of this measure is to compare the results of different resource management heuristics that are trying to achieve the same performance objective but with different approaches. This research was supported by the DARPA/ITO Quorum Program, by the DARPA/ISO BADD Program and the Office of Naval Research under ONR grant number N00014-97-1-0804, by the DARPA/ITO AICE program under contract numbers DABT63-99-C-0010 and DABT63-99-C-0012, and by the Colorado State University George T. Abell Endowment. Intel and Microsoft donated some of the equipment used in this research. Jong-Kook Kim is pursuing a Ph.D. degree from the School of Electrical and Computer Engineering at Purdue University (expected in August 2004). Jong-Kook received his M.S. degree in electrical and computer engineering from Purdue University in May 2000. He received his B.S. degree in electronic engineering from Korea University, Seoul, Korea in 1998. He has presented his work at several international conferences and has been a reviewer for numerous conferences and journals. His research interests include heterogeneous distributed computing, computer architecture, performance measure, resource management, evolutionary heuristics, and power-aware computing. He is a student member of the IEEE, IEEE Computer Society, and ACM. Debra Hensgen is a member of the Research and Evaluation Team at OpenTV in Mountain View, California. OpenTV produces middleware for set-top boxes in support of interactive television. She received her Ph.D. in the area of Distributed Operating Systems from the University of Kentucky. Prior to moving to private industry, as an Associate Professor in the systems area, she worked with students and colleagues to design and develop tools and systems for resource management, network re-routing algorithms and systems that preserve quality of service guarantees, and visualization tools for performance debugging of parallel and distributed systems. She has published numerous papers concerning her contributions to the Concurra toolkit for automatically generating safe, efficient concurrent code, the Graze parallel processing performance debugger, the SAAM path information base, and the SmartNet and MSHN Resource Management Systems. Taylor Kidd is currently a Software Architect for Vidiom Systems in Portland Oregon. His current work involves the writing of multi-company industrial specifications and the architecting of software systems for the digital cable television industry. He has been involved in the establishment of international specifications for digital interactive television in both Europe and in the US. Prior to his current position, Dr. Kidd has been a researcher for the US Navy as well as an Associate Professor at the Naval Postgraduate School. Dr Kidd received his Ph.D. in Electrical Engineering in 1991 from the University of California, San Diego. H. J. Siegel was appointed the George T. Abell Endowed Chair Distinguished Professor of Electrical and Computer Engineering at Colorado State University (CSU) in August 2001, where he is also a Professor of Computer Science. In December 2002, he became the first Director of the CSU Information Science and Technology Center (ISTeC). ISTeC is a university-wide organization for promoting, facilitating, and enhancing CSU’s research, education, and outreach activities pertaining to the design and innovative application of computer, communication, and information systems. From 1976 to 2001, he was a professor at Purdue University. He received two BS degrees from MIT, and the MA, MSE, and PhD degrees from Princeton University. His research interests include parallel and distributed computing, heterogeneous computing, robust computing systems, parallel algorithms, parallel machine interconnection networks, and reconfigurable parallel computer systems. He has co-authored over 300 published papers on parallel and distributed computing and communication, is an IEEE Fellow, is an ACM Fellow, was a Coeditor-in-Chief of the Journal of Parallel and Distributed Computing, and was on the Editorial Boards of both the IEEE Transactions on Parallel and Distributed Systems and the IEEE Transactions on Computers. He was Program Chair/Co-Chair of three major international conferences, General Chair/Co-Chair of four international conferences, and Chair/Co-Chair of five workshops. He has been an international keynote speaker and tutorial lecturer, and has consulted for industry and government. David St. John is Chief Information Officer for WeatherFlow, Inc., a weather services company specializing in coastal weather observations and forecasts. He received a master’s degree in Engineering from the University of California, Irvine. He spent several years as the head of staff on the Management System for Heterogeneous Networks project in the Computer Science Department of the Naval Postgraduate School. His current relationship with cluster computing is as a user of the Regional Atmospheric Modeling System (RAMS), a numerical weather model developed at Colorado State University. WeatherFlow runs RAMS operationally on a Linux-based cluster. Cynthia Irvine is a Professor of Computer Science at the Naval Postgraduate School in Monterey, California. She received her Ph.D. from Case Western Reserve University and her B.A. in Physics from Rice University. She joined the faculty of the Naval Postgraduate School in 1994. Previously she worked in industry on the development of high assurance secure systems. In 2001, Dr. Irvine received the Naval Information Assurance Award. Dr. Irvine is the Director of the Center for Information Systems Security Studies and Research at the Naval Postgraduate School. She has served on special panels for NSF, DARPA, and OSD. In the area of computer security education Dr. Irvine has most recently served as the general chair of the Third World Conference on Information Security Education and the Fifth Workshop on Education in Computer Security. She co-chaired the NSF workshop on Cyber-security Workforce Needs Assessment and Educational Innovation and was a participant in the Computing Research Association/NSF sponsored Grand Challenges in Information Assurance meeting. She is a member of the editorial board of the Journal of Information Warfare and has served as a reviewer and/or program committee member of a variety of security related conferences. She has written over 100 papers and articles and has supervised the work of over 80 students. Professor Irvine is a member of the ACM, the AAS, a life member of the ASP, and a Senior Member of the IEEE. Timothy E. Levin is a Research Associate Professor at the Naval Postgraduate School. He has spent over 18 years working in the design, development, evaluation, and verification of secure computer systems, including operating systems, databases and networks. His current research interests include high assurance system design and analysis, development of models and methods for the dynamic selection of QoS security attributes, and the application of formal methods to the development of secure computer systems. Viktor K. Prasanna received his BS in Electronics Engineering from the Bangalore University and his MS from the School of Automation, Indian Institute of Science. He obtained his Ph.D. in Computer Science from the Pennsylvania State University in 1983. Currently, he is a Professor in the Department of Electrical Engineering as well as in the Department of Computer Science at the University of Southern California, Los Angeles. He is also an associate member of the Center for Applied Mathematical Sciences (CAMS) at USC. He served as the Division Director for the Computer Engineering Division during 1994–98. His research interests include parallel and distributed systems, embedded systems, configurable architectures and high performance computing. Dr. Prasanna has published extensively and consulted for industries in the above areas. He has served on the organizing committees of several international meetings in VLSI computations, parallel computation, and high performance computing. He is the Steering Co-chair of the International Parallel and Distributed Processing Symposium [merged IEEE International Parallel Processing Symposium (IPPS) and the Symposium on Parallel and Distributed Processing (SPDP)] and is the Steering Chair of the International Conference on High Performance Computing(HiPC). He serves on the editorial boards of the Journal of Parallel and Distributed Computing and the Proceedings of the IEEE. He is the Editor-in-Chief of the IEEE Transactions on Computers. He was the founding Chair of the IEEE Computer Society Technical Committee on Parallel Processing. He is a Fellow of the IEEE. Richard F. Freund is the originator of GridIQ’s network scheduling concepts that arose from mathematical and computing approaches he developed for the Department of Defense in the early 1980’s. Dr. Freund has over twenty-five years experience in computational mathematics, algorithm design, high performance computing, distributed computing, network planning, and heterogeneous scheduling. Since 1989, Dr. Freund has published over 45 journal articles in these fields. He has also been an editor of special editions of IEEE Computer and the Journal of Parallel and Distributed Computing. In addition, he is a founder of the Heterogeneous Computing Workshop, held annually in conjunction with the International Parallel Processing Symposium. Dr. Freund is the recipient of many awards, which includes the prestigious Department of Defense Meritorious Civilian Service Award in 1984 and the Lauritsen-Bennet Award from the Space and Naval Warfare Systems Command in San Diego, California.     

Jordan Raff

Jordan Raff is a Cancer Research UK funded group leader at the Wellcome/CR-UK Gurdon Institute in Cambridge, England. He obtained his PhD from the Department of Biochemistry at Imperial College, London, and he worked as a Post-doctoral fellow at the Department of Biophysics and Biochemistry, University of California, San Francisco. He is currently a Director of the Company of Biologists, and on the committee of the British Society of Cell Biology. He has studied centrosomes and cell division in fruit flies throughout his scientific career.     

A clinician's experiences on the Internet.

Dr. John Doyle, a Toronto anesthetist, shares some recent experiences on the Internet. He explains how he became involved and how electronic mail and computer resources help in his daily clinical practice. He also explains how he and other clinicians share opinions, expertise and advice through an Internet-based discussion group devoted to his specialty.     

On the trail of Dr. Fifer.

A gift from a patient drew Hope, BC, family physician Gerd Asche irrevocably into the local medical history of the 1858 Fraser River Gold Rush. Because of his interest in Dr. Max William Fifer, Asche undertook research missions in British Columbia, England and the US, converted his computer room to a research and writing centre, and wrote a biography of his predecessor and colleague. He recounts his experience and the growing satisfaction provided by his interest in medical history.     

Cell volume regulation and ischemic tissue damage

Over years of friendly meetings with Professor Aharon Katzir-Katchalsky, many topics of mutual interest were discussed. He was the ideal person to come to with a problem. After being subjected to his critical, analytic mind, most research problems seemed simple, more clearly defined and understandable. His broad biologic and scientific background grew from an apparently insatiable interest in all natural phenomena. He generously shared his knowledge and imparted his wisdom with a share of his own infectious excitement. He was quick to sense the significance of understanding of biological processes to their practical application. For this reason it seems appropriate to relate the progress made in the understanding of cell volume regulation, which had been discussed on several occasions with him, to its possible significance as a factor in disease processes.Dr. Frega is a Fellow of the National Kidney Foundation, Inc., 1972–73.     

Metabolism of Rhizobium Bacteroids

Nitrogen fixation within legume nodules results from a complex metabolic exchange between bacteria of the family Rhizobiaciae and the plant host. Carbon is supplied to the differentiated bacterial cells, termed bacteroids, in the form of dicarboxylic acids to fuel nitrogen fixation. In exchange, fixed nitrogen is transferred to the plant. Both the bacteroid and the plant-derived peribacteroid membrane tightly regulate the exchange of metabolites. In the bacteroid oxidation of dicarboxylic acids via the TCA cycle occurs in an oxygenlimited environment. This restricts the TCA cycle at key points, such as the 2-oxoglutarate dehydrogenase complex, and requires that inputs of carbon and reductant are balanced with outputs from the TCA cycle. This may be achieved by metabolism through accessory pathways that can remove intermediates, reductant, or ATP from the cycle. These include synthesis of the carbon polymers PHB and glycogen and bypass pathways such as the recently identified 2-oxoglutarate decarboxylase reaction in soybean bacteroids. Recent labeling data have shown that bacteroids synthesize and secrete amino acids, which has led to controversy over the role of amino acids in nodule metabolism. Here we review bacteroid carbon metabolism in detail, evaluate the labeling studies that relate to amino acid metabolism by bacteroids, and place the work in context with the genome sequences of Mesorhizobium loti and Sinorhizobium meliloti. We also consider a wider range of metabolic pathways that are probably of great importance to rhizobia in the rhizosphere, during nodule initiation, infection thread development, and bacteroid development. Referee: Dr. Robert Ludwig, Department of Molecular, Celluar, and Developmental Biology, Sinheimer Laboratories, University of California, Santa Cruz, CA 95064     

A Collaborative Informatics Infrastructure for Multi-Scale Science

The Collaboratory for Multi-scale Chemical Science (CMCS) is developing a powerful informatics-based approach to synthesizing multi-scale information in support of systems-based research and is applying it within combustion science. An open source multi-scale informatics toolkit is being developed that addresses a number of issues core to the emerging concept of knowledge grids including provenance tracking and lightweight federation of data and application resources into cross-scale information flows. The CMCS portal is currently in use by a number of high-profile pilot groups and is playing a significant role in enabling their efforts to improve and extend community maintained chemical reference information. James D. Myers received his B.A. in Physics from Cornell University in 1985 and his Ph.D. in Chemistry from the University of California at Berkeley in 1993. He is currently the Associate Director for Collaborative Technologies at the National Center for Supercomputing Applications (NCSA) at the University of Illinois, Urbana Champaign. Dr. Myers is the lead investigator on the U.S. Department of Energy (DOE) sponsored Scientific Annotation Middleware project (http://www.scidac.org/SAM/) (scientific content management, semantic annotation, and records functionality) and is serving as the Chief Technical Officer for the DOE-sponsored Collaboratory for Multiscale Chemical Science (CMCS) project. His is also the lead architect for the Mid-America Earthquake Center's MAEViz hazard risk management collaboratory and co-lead of NCSA's Collaborative Large-scale Engineering Analysis Network for Environmental Research (CLEANER) related cybercollaboratory effort. Open source software developed by Dr. Myers and his colleagues including the electronic laboratory notebook (ELN) and the Collaborative Research Environment (CORE) real-time collaboration environment have been downloaded from the Pacific Northwest National Laboratory (PNNL) Collaboratory website (http://collaboratory.pnl.gov) by thousands of researchers and educators. Due to space limitations, individual bios for all 28 authors are not shown. The CMCS project is led by Dr. Larry Rahn (rahn@sandia.gov) at Sandia National Laboratories. The team includes combustion researchers and computer science researchers and developers at five DOE National Laboratories (Argonne, Lawrence Livermore, Los Alamos, Pacific Northwest, and Sandia National Laboratories), the National Institute of Standards and Technology, Massachusetts Institute of Technology, and the University of California, Berkeley. Current contact information and biographic information for team members is available at http://cmcs.org/team.php.     

邹承鲁先生两项被收入教科书的研究成果

邹承鲁先生出生于1923年5月17日，1951年于英国剑桥大学获博士学位。他长期从事蛋白质结构与功能的研究，作为近代中国生物化学的奠基人之一，在酶学研究领域做出了具有重要意义的工作。为了纪念邹承鲁先生诞辰100周年，特将邹先生60年前完成的两项重要的研究成果（蛋白质必需基团修饰程度和活性丧失的定量关系，酶活性不可逆抑制动力学）较详细地介绍给读者。希望通过本文的介绍，使读者看到老一辈科学家“是如何在资源匮乏的条件下，运用自己的聪明才智取得成就”的范例。     

A conversation with John Sulston

Sir John Sulston was a co-winner of the Nobel Prize for Medicine in 2002. He won the prize for his discoveries concerning "genetic regulation of organ development and programmed cell death," along with his colleagues sydney Brenner and H. Robert Horvitz. Dr. Sulston was founding director of the Sanger Centre, Cambridge, England, which he headed from 1992 to 2000. From 1993 to 2000, he led the British arm of the international team selected to work on the Human Genome Project. He is co-author of the book The Common Thread: A Story of Science, Politics, Ethics, and the Human Genome, published by Joseph Henry Press in 2002.This interview was conducted on December 20, 2002, shortly after Dr. Sulston was awarded his Nobel Prize and was originally broadcast on that date on radio station WPKN-FM in Bridgeport, Connecticut. The interview was conducted by Valerie Richardson, the Managing Editor of The Yale Journal of Biology and Medicine.Dr. Sulston has been an outspoken advocate against letting the data from the Human Genome Project become property of commercial interests that would charge the world's scientific community for its use. Since leaving the Sanger Institute, he has worked with OxFam, the Oxford Campaign for Famine Relief.     

Warmest Congratulations to Dr. Yuan-Cheng Fung at His Centennial Celebration

Professor Y.C. Fung has made tremendous impacts on science, engineering and humanity through his research and its applications, by setting the highest standards, through educating many students and their students, and providing his exemplary leadership. He has applied his profound knowledge and elegant analytical methods to the study of biomedical problems with rigor and excellence. He established the foundations of biomechanics in living tissues and organs. Through his vision of the power of “making models” to explain and predict biological phenomena, Dr. Fung opened up new vista for bioengineering, from organs-systems to molecules-genes, and has provided the foundation of research activities in many institutions in the United States and the world. He has made outstanding contributions to education in bioengineering, service to professional organizations, and translation to industry and clinical medicine. He is widely recognized as the Father of Biomechanics and the leading Bioengineer in the world. His extraordinary achievements and commands in science, engineering and the arts make him a Renaissance Man for the world.     

Henk van den Bosch: chemist and biochemist

Henk van den Bosch is a native of The Netherlands and recently retired from his position as Professor at Utrecht University. This article summarizes the many scientific achievements of Dr. van den Bosch. He enjoys an international reputation for his research on phospholipases A, cardiolipin biosynthesis in eukaryotes, lysophospholipases, phosphatidylcholine biosynthesis for lung surfactant, plasmalogen biosynthesis in peroxisomes, diagnosis of peroxisomal disorders and most recently his work on alkyl-dihydroxyacetone phosphate synthase. During his research career Henk van den Bosch published approximately 280 articles and presented 110 invited lectures.     

A surgeon with AIDS made the most of borrowed time.

Dr. Orville Messenger and his wife, Dorothy wrote a book, Borrowed Time, which chronicled his decade-long struggle with AIDS. The disease developed following a 1985 blood transfusion. A general and thoracic surgeon who also worked for the Canadian Medical Protective Association, Dr. Messenger wrote the book to raise public awareness, and money for AIDS research, prevention and treatment. He died Dec. 13, 1995--exactly 10 years after being told to take a blood test because of possible HIV infection.     

Q & A. [interview

George Oster is Professor of Biophysics, University of California, Berkeley. He received his B.S. at the U.S. Merchant Marine Academy and his Ph.D. at Columbia University. He began his career in biophysics as a postdoc at the Weizmann Institute under Aharon Katchalsky, where his research involved membrane biophysics and irreversible thermodynamics. His concern for environmental issues led him into population biology, which shaded into evolutionary biology and thence to developmental biology, cell biology and, most recently, protein motors and bacterial motility and pattern formation. His tools are mathematics, physics and computer simulation. He is currently a faculty member in the Departments of Molecular and Cellular Biology and the College of Natural Resources at Berkeley.     

Dr. Jon Gerrard's attention switches from federal cabinet to evidence-based child care

Dr. Jon Gerrard, a Winnipeg pediatrician who went from the heights of political success with a post in the federal cabinet to a narrow defeat in the 1997 federal election, is now devoting his attention to improving health care for children. He thinks the internet can play a lead role in these improvements.     

A physiological study of formate dehydrogenase,formate oxidase and hydrogenlyase fromEscherichia coli K-12

Escherichia coli was grown under various culture conditions. Variations in the levels of formate dehydrogenase which reacts with methylene blue (MB) or phenazine methosulfate (PMS) (N enzyme), formate dehydrogenase which reacts with benzyl viologen (BV) (H enzyme), formate oxidase and hydrogenlyase were analyzed. It was observed that formate dehydrogenase N and formate oxidase were induced by nitrate and repressed by oxygen. Synthesis of formate dehydrogenase H and hydrogenlyase was induced by formate and repressed by nitrate and oxygen. Selenite was required for the biosynthesis of formate dehydrogenase H and hydrogenlyase. Activity of both formate oxidase and hydrogenlyase was inhibited by azide and KCN but not by N-heptyl hydroxyquinoline-N-oxide (HOQNO); on the other hand, formate oxidase was extremely sensitive to HOQNO. Data were obtained which suggest that cytochromes are not involved in hydrogen formation from formate. Part of this work was carried out when the senior author was visiting Research Biologist in the Laboratory of Dr. J. A. de Mosss at the University of California, San Diego. Thanks are given to Dr. De Moss for his hospitality and advise and to Dr. Warren Butler of the University of California, San Diego for making available his spectrophotometer to carry out cytochrome analyses. Most of this work was sustained by a grant from the Research Corporation, Brown Hazen Fund and the financial help of the C.O.F.A.A. from the Instituto Politécnico Nacional.